Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

Franks, Steven J.; Perez‐Sweeney, Beatriz; Strahl, Maya; Nowogrodzki, Anna; Weber, Joseph T.; Lalchan, Rebecca; Jordan, Kevin P; Litt, Amy

doi:10.7287/peerj.preprints.1430

Cited by 4 publications

(5 citation statements)

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“…We propose that early expression of genes repressed by FLC paralogs, such as SOC1 and SPL15, might contribute to early owering in these F 3 lines due to the br c-y allele. Franks et al (2015) reported that the total amount of SOC1 expressed is strongly correlated with owering time. If a SOC1 allele circumventing FLC repression is identi ed, early-owering can be accelerated further by combining this with BrFT2-C.…”

Section: Discussionmentioning

confidence: 99%

Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T

Nishikawa

Tamiru

Hara

et al. 2023

Preprint

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Controlling the timing of flowering is key to improving yield and quality of several agricultural crops including the Brassicas. Many Brassicaceae plants possess a conserved flowering mechanism in which FLOWERING LOCUS C (FLC) represses the transcription of flowering activators, such as FLOWERING LOCUS T (FT), during vernalization. Here, we employed genetic analysis based on next-generation sequencing to identify a dominate FT allele, BrFT2-C, for flowering in the absence of vernalization in the Brassica rapa cultivar ‘CHOY SUM EX CHINA 3’. BrFT2-C harbors two large insertions upstream of its coding region and is constitutively expressed without vernalization, despite FLCexpression. We show that BrFT2-C offers an opportunity to introduce flowering without vernalization requirement into winter-type brassica crops, including B. napus, which have many functional FLC paralogs. Furthermore, we demonstrated the feasibility of using B. rapa harboring BrFT2-C as rootstock for grafting to induce flowering in radish (Raphanus sativus), which requires vernalization for flowering. We believe that the ability of BrFT2-C to overcome repression by FLCcan have significant applications in brassica crops breeding to increase yields by accelerating or delaying flowering.

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Section: Discussionmentioning

confidence: 99%

Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T

Nishikawa

Tamiru

Hara

et al. 2023

Preprint

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“…Plant flowering is a coherent and complex process, and flowering-related genes such as SEP , APETALA , AG , and AGL comprehensively regulate flower formation [ 47 ]. Numerous studies have shown that FLC can block the transcriptional activation of SOC1 and requires SVP expression to delay flowering [ 48 ]. In the present study, the fluorescence quantitative results showed that the expression levels of PdMADS47 ( SVP ) and PdMADS16 ( AGL12 ) were significantly increased in the dormant stage of ‘Nonpareil’ almond flower buds, while PdMADS35 ( FLC ) and PdMADS23 ( SOC1 ) were expressed at a normal level in B1.…”

Section: Discussionmentioning

confidence: 99%

“…PdMADS family member protein interaction analysis can predict the functions of these genes [ 42 ]. SOC1 is an important gene for regulating flowering, and its overexpression can suppress late flowering in plants with functional FRI and FLC alleles [ 48 ]. Notably, this study found that SOC1 ( PdMADS23 , 26 , and 39 ) interacts with multiple groups of genes, such as SEP ( PdMADS42 ), APETALA3 ( PdMADS61 ), and AGAMOUS ( PdMADS36 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Almond Reveal Its Expression Features in Different Flowering Periods

Liu

Zhang

et al. 2022

Genes

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The MADS-box gene family is an important family of transcription factors involved in multiple processes, such as plant growth and development, stress, and in particular, flowering time and floral organ development. Almonds are the best-selling nuts in the international fruit trade, accounting for more than 50% of the world’s dried fruit trade, and one of the main economic fruit trees in Kashgar, Xinjiang. In addition, almonds contain a variety of nutrients, such as protein and dietary fiber, which can supplement nutrients for people. They also have the functions of nourishing the yin and kidneys, improving eyesight, and strengthening the brain, and they can be applied to various diseases. However, there is no report on the MADS-box gene family in almond (Prunus dulcis). In this study, a total of 67 PdMADS genes distributed across 8 chromosomes were identified from the genome of almond ‘Wanfeng’. The PdMADS members were divided into five subgroups—Mα, Mβ, Mγ, Mδ, and MIKC—and the members in each subgroup had conserved motif types and exon and intron numbers. The number of exons of PdMADS members ranged from 1 to 20, and the number of introns ranged from 0 to 19. The number of exons and introns of different subfamily members varied greatly. The results of gene duplication analysis showed that the PdMADS members had 16 pairs of segmental duplications and 9 pairs of tandem duplications, so we further explored the relationship between the MADS-box gene members in almond and those in Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persica based on colinear genes and evolutionary selection pressure. The results of the cis-acting elements showed that the PdMADS members were extensively involved in a variety of processes, such as almond growth and development, hormone regulation, and stress response. In addition, the expression patterns of PdMADS members across six floral transcriptome samples from two almond cultivars, ‘Wanfeng’ and ‘Nonpareil’, had significant expression differences. Subsequently, the fluorescence quantitative expression levels of the 15 PdMADS genes were highly similar to the transcriptome expression patterns, and the gene expression levels increased in the samples at different flowering stages, indicating that the two almond cultivars expressed different PdMADS genes during the flowering process. It is worth noting that the difference in flowering time between ‘Wanfeng’ and ‘Nonpareil’ may be caused by the different expression activities of PdMADS47 and PdMADS16 during the dormancy period, resulting in different processes of vernalization. We identified a total of 13,515 target genes in the genome based on the MIKC DNA-binding sites. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on the PdMADS gene family and investigated six flowering samples from two almond cultivars, the early-flowering ‘Wanfeng’ and late-flowering ‘Nonpareil’, for quantitative expression level identification. These findings lay a foundation for future in-depth studies on the mechanism of PdMADS gene regulation during flowering in different almond cultivars.

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“…B. rapa has been sequenced and annotated (Zhang et al, 2018). B. rapa is closely related to A. thaliana (Cheng et al, 2014; Franks et al, 2015; Wang et al, 2011), but is self‐incompatible and reproduces only by outcrossing. The B. rapa population we used in this study originated from the San Joaquin Marsh Reserve in Orange County, CA in 1997 (Franks et al, 2007), and seeds were collected after several years of greater than average precipitation.…”

Section: Methodsmentioning

confidence: 99%

Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

Johnson

Tittes

Franks

2023

J of Evolutionary Biology

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Rapid evolution to environmental conditions has been documented by a number of studies (Franks et al., 2014;Hendry & Kinnison, 1999). However, the genomic basis of rapid evolution is less often characterized yet is fundamentally important as it can allow identification of adaptive loci and possible genetic pathways that increase fitness (Franks & Hoffmann, 2012). Studies that explore the genomic basis of rapid adaptation often find changes in many polymorphic loci. For example, adaptation to climate has been tied to subtle shifts in allele frequencies across many loci in the thale cress A. thaliana (Hancock et al., 2011), the stickleback G. aculeatus (Roberts Kingman et al., 2021), and the mouse M. musculus (Ferris et al., 2021). These examples suggest that rapid adaptation may often occur through changes in standing variation (Messer & Petrov, 2013;Pritchard et al., 2010).While progress has been made toward understanding the genomic basis of rapid adaptation, less is known about the consistency of genomic shifts underlying rapid evolution (Blount et al., 2018;Lobkovsky & Koonin, 2012). If rapid evolution is driven by selection, genetically similar populations under the same environment are likely to evolve similar outcomes (parallel evolution). However,

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Variation in the flowering time orthologs BrFLC and BrSOC1 in a natural population of Brassica rapa

Cited by 4 publications

References 54 publications

Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T

Non-vernalization requirement for flowering in Brassica rapa conferred by a dominant allele of FLOWERING LOCUS T

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Almond Reveal Its Expression Features in Different Flowering Periods

Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

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